# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Thu Jul 22 06:34:39 2021
#   Inital geometry file: a 147 line input string
#   Ligand name: (4~{R})-~{N}-[3-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)propyl]-4-methyl-2-oxidanylidene-1,3,4,5-tetrahydro-1,5-benzodiazepine-6-carboxamide
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: COc1ccc2CCCN(CCCNC(=O)c3cccc4NC(=O)C[C@@H](C)Nc34)c2c1
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 OS8  OS8  (4~{R})-~{N}-[3-(7-methoxy-3,4-dihydro-2~{H}-quinolin-1-yl)propyl]-4-methyl-2-oxidanylidene-1,3,4,5-tetrahydro-1,5-benzodiazepine-6-carboxamide  ligand  61  31  .  2022-03-23  2022-03-23
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as PERFECT
;

data_comp_OS8
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 OS8  C4   C  C     0   0.499  26.6957  34.7777  26.9687
 OS8  C14  C  CH2   0  -0.284  26.8964  44.9346  21.9844
 OS8  C5   C  CR6   0   0.334  26.2944  37.2055  27.0492
 OS8  C6   C  CR16  0  -0.321  25.9807  38.1334  28.0300
 OS8  C11  C  CH2   0  -0.304  29.2038  41.2224  23.4017
 OS8  C7   C  CR16  0  -0.255  26.2274  39.4824  27.8312
 OS8  C8   C  CR16  0  -0.315  26.8280  39.8941  26.6572
 OS8  C9   C  CR6   0  -0.113  27.1783  38.9757  25.6658
 OS8  C10  C  C     0   0.547  27.8048  39.4701  24.4034
 OS8  C12  C  CH2   0  -0.462  28.1945  42.0537  22.6156
 OS8  C13  C  CH2   0  -0.321  27.4645  43.0778  23.4839
 OS8  N1   N  NH1   0  -0.704  25.9357  35.8653  27.2499
 OS8  N2   N  NH1   0  -0.638  28.6223  40.5244  24.5323
 OS8  C3   C  CH2   0  -0.623  28.0627  35.0798  26.4143
 OS8  N3   N  NT    0  -0.526  26.4379  43.8191  22.7896
 OS8  C1   C  CH3   0  -0.662  27.6423  34.4692  23.9968
 OS8  C2   C  CH1   0  -0.091  28.0130  35.5748  24.9718
 OS8  C15  C  CH2   0  -0.463  25.7805  45.9360  21.7624
 OS8  C16  C  CH2   0  -0.477  24.6284  45.2528  21.0474
 OS8  C17  C  CR6   0  -0.015  24.2740  43.9499  21.7155
 OS8  C18  C  CR16  0  -0.294  23.0155  43.3937  21.5322
 OS8  C19  C  CR16  0  -0.380  22.6244  42.1987  22.1093
 OS8  C20  C  CR6   0   0.397  23.5400  41.5243  22.9142
 OS8  C21  C  CR16  0  -0.510  24.8083  42.0517  23.1242
 OS8  C22  C  CR6   0   0.417  25.1969  43.2741  22.5407
 OS8  O1   O  O2    0  -0.479  23.1155  40.3587  23.4494
 OS8  C23  C  CH3   0  -0.441  23.9951  39.6164  24.2665
 OS8  O2   O  O     0  -0.501  27.5739  38.9567  23.3090
 OS8  C24  C  CR6   0   0.268  26.8761  37.6094  25.8321
 OS8  N4   N  NH1   0  -0.681  27.0525  36.6689  24.8263
 OS8  O3   O  O     0  -0.473  26.2890  33.6468  27.1780
 OS8  H2   H  HCH2  0   0.242  27.7264  45.4073  22.5120
 OS8  H3   H  HCR6  0   0.274  25.5169  37.7931  28.9477
 OS8  H4   H  HCH2  0   0.257  29.6932  40.5089  22.7365
 OS8  H5   H  HCH2  0   0.256  29.9859  41.8651  23.8058
 OS8  H6   H  HCR6  0   0.264  25.9535  40.2043  28.5879
 OS8  H7   H  HCR6  0   0.264  27.0045  40.9517  26.5055
 OS8  H8   H  HCH2  0   0.241  27.4755  41.3961  22.1232
 OS8  H9   H  HCH2  0   0.246  28.7386  42.5686  21.8188
 OS8  H10  H  HCH2  0   0.253  28.1844  43.8009  23.8762
 OS8  H11  H  HCH2  0   0.240  27.0353  42.5961  24.3647
 OS8  H12  H  HNH1  0   0.402  25.0682  35.6901  27.7386
 OS8  H13  H  HNH1  0   0.413  28.8677  40.8434  25.4542
 OS8  H14  H  HCH2  0   0.285  28.6682  34.1755  26.4562
 OS8  H15  H  HCH2  0   0.285  28.5554  35.8256  27.0448
 OS8  H16  H  HCH3  0   0.232  28.3845  33.6713  24.0188
 OS8  H17  H  HCH3  0   0.229  26.6672  34.0406  24.2319
 OS8  H18  H  HCH3  0   0.238  27.6008  34.8544  22.9769
 OS8  H19  H  HCH1  0   0.245  29.0248  35.9254  24.7269
 OS8  H20  H  HCH2  0   0.241  26.1544  46.7774  21.1772
 OS8  H21  H  HCH2  0   0.231  25.4524  46.3325  22.7270
 OS8  H22  H  HCH2  0   0.244  23.7527  45.9051  21.0187
 OS8  H23  H  HCH2  0   0.236  24.9094  45.0764  20.0037
 OS8  H24  H  HCR6  0   0.241  22.3080  43.9245  20.9046
 OS8  H25  H  HCR6  0   0.245  21.6344  41.7939  21.9440
 OS8  H26  H  HCR6  0   0.261  25.5069  41.5089  23.7419
 OS8  H27  H  HCH3  0   0.259  23.4508  38.7293  24.5830
 OS8  H28  H  HCH3  0   0.221  24.8911  39.2985  23.7271
 OS8  H29  H  HCH3  0   0.222  24.3003  40.1724  25.1578
 OS8  H30  H  HNH1  0   0.384  27.1722  37.1246  23.9310
 OS8  H1   H  HCH2  0   0.219  27.2867  44.5981  21.0138

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 OS8  C16  C15  single    1.518  0.020  1.518
 OS8  C16  C17  single    1.506  0.020  1.506
 OS8  C15  C14  single    1.516  0.020  1.516
 OS8  C18  C17  aromatic  1.388  0.020  1.388
 OS8  C18  C19  aromatic  1.383  0.020  1.383
 OS8  C17  C22  aromatic  1.410  0.020  1.410
 OS8  C14  N3   single    1.450  0.020  1.450
 OS8  C19  C20  aromatic  1.393  0.020  1.393
 OS8  C22  N3   single    1.378  0.020  1.378
 OS8  C22  C21  aromatic  1.409  0.020  1.409
 OS8  N3   C13  single    1.444  0.020  1.444
 OS8  C12  C13  single    1.528  0.020  1.528
 OS8  C12  C11  single    1.526  0.020  1.526
 OS8  C20  C21  aromatic  1.390  0.020  1.390
 OS8  C20  O1   single    1.351  0.020  1.351
 OS8  C1   C2   single    1.520  0.020  1.520
 OS8  O2   C10  double    1.231  0.020  1.231
 OS8  C11  N2   single    1.450  0.020  1.450
 OS8  O1   C23  single    1.411  0.020  1.411
 OS8  C2   N4   single    1.463  0.020  1.463
 OS8  C2   C3   single    1.526  0.020  1.526
 OS8  N4   C24  single    1.388  0.020  1.388
 OS8  C10  N2   single    1.340  0.020  1.340
 OS8  C10  C9   single    1.494  0.020  1.494
 OS8  C24  C9   aromatic  1.409  0.020  1.409
 OS8  C24  C5   aromatic  1.408  0.020  1.408
 OS8  C3   C4   single    1.506  0.020  1.506
 OS8  C9   C8   aromatic  1.396  0.020  1.396
 OS8  O3   C4   double    1.220  0.020  1.220
 OS8  C4   N1   single    1.356  0.020  1.356
 OS8  N1   C5   single    1.402  0.020  1.402
 OS8  C5   C6   aromatic  1.386  0.020  1.386
 OS8  C8   C7   aromatic  1.382  0.020  1.382
 OS8  C6   C7   aromatic  1.386  0.020  1.386
 OS8  C14  H1   single    0.970  0.020  1.090
 OS8  C14  H2   single    0.970  0.020  1.090
 OS8  C6   H3   single    0.930  0.020  1.080
 OS8  C11  H4   single    0.970  0.020  1.090
 OS8  C11  H5   single    0.970  0.020  1.090
 OS8  C7   H6   single    0.930  0.020  1.080
 OS8  C8   H7   single    0.930  0.020  1.080
 OS8  C12  H8   single    0.970  0.020  1.090
 OS8  C12  H9   single    0.970  0.020  1.090
 OS8  C13  H10  single    0.970  0.020  1.090
 OS8  C13  H11  single    0.970  0.020  1.090
 OS8  N1   H12  single    0.860  0.020  1.020
 OS8  N2   H13  single    0.860  0.020  1.020
 OS8  C3   H14  single    0.970  0.020  1.090
 OS8  C3   H15  single    0.970  0.020  1.090
 OS8  C1   H16  single    0.970  0.020  1.090
 OS8  C1   H17  single    0.970  0.020  1.090
 OS8  C1   H18  single    0.970  0.020  1.090
 OS8  C2   H19  single    0.970  0.020  1.090
 OS8  C15  H20  single    0.970  0.020  1.090
 OS8  C15  H21  single    0.970  0.020  1.090
 OS8  C16  H22  single    0.970  0.020  1.090
 OS8  C16  H23  single    0.970  0.020  1.090
 OS8  C18  H24  single    0.930  0.020  1.080
 OS8  C19  H25  single    0.930  0.020  1.080
 OS8  C21  H26  single    0.930  0.020  1.080
 OS8  C23  H27  single    0.970  0.020  1.090
 OS8  C23  H28  single    0.970  0.020  1.090
 OS8  C23  H29  single    0.970  0.020  1.090
 OS8  N4   H30  single    0.890  0.020  1.040

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 OS8  O3   C4   C3   123.50  3.000
 OS8  O3   C4   N1   121.39  3.000
 OS8  C3   C4   N1   115.10  3.000
 OS8  H2   C14  H1   106.84  3.000
 OS8  H2   C14  C15  110.16  3.000
 OS8  H1   C14  C15  109.53  3.000
 OS8  H2   C14  N3   107.78  3.000
 OS8  H1   C14  N3   111.54  3.000
 OS8  C15  C14  N3   110.90  3.000
 OS8  C24  C5   N1   120.24  3.000
 OS8  N1   C5   C6   118.73  3.000
 OS8  C24  C5   C6   120.87  3.000
 OS8  H3   C6   C7   120.24  3.000
 OS8  H3   C6   C5   119.09  3.000
 OS8  C7   C6   C5   120.65  3.000
 OS8  H5   C11  H4   106.85  3.000
 OS8  H5   C11  N2   106.41  3.000
 OS8  H4   C11  N2   109.89  3.000
 OS8  H5   C11  C12  110.15  3.000
 OS8  H4   C11  C12  109.81  3.000
 OS8  N2   C11  C12  113.49  3.000
 OS8  H6   C7   C8   120.40  3.000
 OS8  H6   C7   C6   120.30  3.000
 OS8  C8   C7   C6   119.30  3.000
 OS8  H7   C8   C9   120.14  3.000
 OS8  H7   C8   C7   118.74  3.000
 OS8  C9   C8   C7   121.10  3.000
 OS8  C24  C9   C10  120.71  3.000
 OS8  C24  C9   C8   120.01  3.000
 OS8  C10  C9   C8   119.19  3.000
 OS8  O2   C10  N2   121.87  3.000
 OS8  N2   C10  C9   115.79  3.000
 OS8  O2   C10  C9   122.33  3.000
 OS8  H9   C12  H8   106.41  3.000
 OS8  H9   C12  C13  109.64  3.000
 OS8  H8   C12  C13  110.20  3.000
 OS8  H9   C12  C11  107.62  3.000
 OS8  H8   C12  C11  109.88  3.000
 OS8  C13  C12  C11  112.86  3.000
 OS8  H11  C13  H10  105.14  3.000
 OS8  H11  C13  N3   109.56  3.000
 OS8  H10  C13  N3   107.52  3.000
 OS8  H11  C13  C12  110.52  3.000
 OS8  H10  C13  C12  109.43  3.000
 OS8  N3   C13  C12  114.23  3.000
 OS8  H12  N1   C5   117.03  3.000
 OS8  H12  N1   C4   116.24  3.000
 OS8  C5   N1   C4   126.41  3.000
 OS8  H13  N2   C10  119.10  3.000
 OS8  H13  N2   C11  117.65  3.000
 OS8  C10  N2   C11  123.24  3.000
 OS8  H15  C3   H14  107.07  3.000
 OS8  H15  C3   C2   109.78  3.000
 OS8  H14  C3   C2   108.89  3.000
 OS8  H15  C3   C4   109.48  3.000
 OS8  H14  C3   C4   108.90  3.000
 OS8  C2   C3   C4   112.56  3.000
 OS8  C22  N3   C13  121.60  3.000
 OS8  C13  N3   C14  115.92  3.000
 OS8  C22  N3   C14  119.26  3.000
 OS8  H18  C1   H17  107.83  3.000
 OS8  H18  C1   H16  107.65  3.000
 OS8  H17  C1   H16  108.47  3.000
 OS8  H18  C1   C2   110.62  3.000
 OS8  H17  C1   C2   111.44  3.000
 OS8  H16  C1   C2   110.70  3.000
 OS8  H19  C2   N4   110.11  3.000
 OS8  H19  C2   C1   108.29  3.000
 OS8  N4   C2   C1   108.66  3.000
 OS8  H19  C2   C3   106.52  3.000
 OS8  N4   C2   C3   110.98  3.000
 OS8  C1   C2   C3   112.24  3.000
 OS8  H21  C15  H20  107.24  3.000
 OS8  H21  C15  C16  110.55  3.000
 OS8  H20  C15  C16  110.76  3.000
 OS8  H21  C15  C14  109.35  3.000
 OS8  H20  C15  C14  109.62  3.000
 OS8  C16  C15  C14  109.29  3.000
 OS8  H23  C16  H22  106.07  3.000
 OS8  H23  C16  C17  110.10  3.000
 OS8  H22  C16  C17  109.85  3.000
 OS8  H23  C16  C15  109.06  3.000
 OS8  H22  C16  C15  110.61  3.000
 OS8  C17  C16  C15  111.03  3.000
 OS8  C22  C17  C18  118.58  3.000
 OS8  C22  C17  C16  121.33  3.000
 OS8  C18  C17  C16  120.08  3.000
 OS8  H24  C18  C19  118.67  3.000
 OS8  H24  C18  C17  118.15  3.000
 OS8  C19  C18  C17  123.18  3.000
 OS8  H25  C19  C20  120.55  3.000
 OS8  H25  C19  C18  121.19  3.000
 OS8  C20  C19  C18  118.26  3.000
 OS8  O1   C20  C21  123.67  3.000
 OS8  O1   C20  C19  116.11  3.000
 OS8  C21  C20  C19  120.23  3.000
 OS8  H26  C21  C22  119.66  3.000
 OS8  H26  C21  C20  119.11  3.000
 OS8  C22  C21  C20  121.22  3.000
 OS8  C21  C22  C17  118.52  3.000
 OS8  C21  C22  N3   121.11  3.000
 OS8  C17  C22  N3   120.36  3.000
 OS8  C23  O1   C20  119.16  3.000
 OS8  H29  C23  H28  108.73  3.000
 OS8  H29  C23  H27  108.48  3.000
 OS8  H28  C23  H27  108.45  3.000
 OS8  H29  C23  O1   112.23  3.000
 OS8  H28  C23  O1   112.22  3.000
 OS8  H27  C23  O1   106.59  3.000
 OS8  N4   C24  C9   122.96  3.000
 OS8  C9   C24  C5   117.95  3.000
 OS8  N4   C24  C5   118.97  3.000
 OS8  H30  N4   C24  110.54  3.000
 OS8  H30  N4   C2   110.32  3.000
 OS8  C24  N4   C2   121.20  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 OS8  CONST_01  C8   C7   C6   C5      0.00   0.0  0
 OS8  CONST_02  C9   C8   C7   C6      0.00   0.0  0
 OS8  CONST_03  C24  C9   C8   C7      0.00   0.0  0
 OS8  CONST_04  C20  C19  C18  C17     0.00   0.0  0
 OS8  CONST_05  C20  C21  C22  C17     0.00   0.0  0
 OS8  CONST_06  C21  C22  C17  C18     0.00   0.0  0
 OS8  CONST_07  C21  C20  C19  C18     0.00   0.0  0
 OS8  CONST_08  C22  C17  C18  C19     0.00   0.0  0
 OS8  CONST_09  C22  C21  C20  C19     0.00   0.0  0
 OS8  CONST_10  C10  C9   C8   C7    180.00   0.0  0
 OS8  CONST_11  O1   C20  C19  C18   180.00   0.0  0
 OS8  CONST_12  O1   C20  C21  C22   180.00   0.0  0
 OS8  CONST_13  H6   C7   C6   C5    180.00   0.0  0
 OS8  CONST_14  H7   C8   C7   C6    180.00   0.0  0
 OS8  CONST_15  H3   C6   C7   C8    180.00   0.0  0
 OS8  CONST_16  H26  C21  C22  N3      0.00   0.0  0
 OS8  CONST_17  H24  C18  C17  C16     0.00   0.0  0
 OS8  CONST_18  H25  C19  C18  C17   180.00   0.0  0
 OS8  CONST_19  C9   C10  N2   C11   180.00   0.0  0
 OS8  CONST_20  H13  N2   C10  C9      0.00   0.0  0
 OS8  CONST_21  O2   C10  N2   C11     0.00   0.0  0
 OS8  Var_01    C17  C16  C15  C14    48.68  30.0  1
 OS8  Var_02    C17  C22  N3   C14   -13.00  30.0  1
 OS8  Var_03    C16  C15  C14  N3    -59.88  30.0  1
 OS8  Var_04    C18  C17  C16  C15   158.33  30.0  1
 OS8  Var_05    C22  N3   C14  C15    42.33  30.0  1
 OS8  Var_06    C12  C13  N3   C14   -80.86  30.0  3
 OS8  Var_07    O2   C10  C9   C8   -144.16  30.0  2
 OS8  Var_08    N3   C13  C12  C11  -176.03  30.0  3
 OS8  Var_09    H27  C23  O1   C20   179.96  30.0  3
 OS8  Var_10    C12  C11  N2   C10    71.54  30.0  2
 OS8  Var_11    N2   C11  C12  C13    56.48  30.0  3

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 OS8  chir_01  C2  C1  N4  C3  negativ

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 OS8  plan-1  N3   0.020
 OS8  plan-1  C16  0.020
 OS8  plan-1  C17  0.020
 OS8  plan-1  C18  0.020
 OS8  plan-1  C19  0.020
 OS8  plan-1  C20  0.020
 OS8  plan-1  C21  0.020
 OS8  plan-1  C22  0.020
 OS8  plan-1  O1   0.020
 OS8  plan-1  H24  0.020
 OS8  plan-1  H25  0.020
 OS8  plan-1  H26  0.020
 OS8  plan-2  C5   0.020
 OS8  plan-2  C6   0.020
 OS8  plan-2  C7   0.020
 OS8  plan-2  C8   0.020
 OS8  plan-2  C9   0.020
 OS8  plan-2  C10  0.020
 OS8  plan-2  N1   0.020
 OS8  plan-2  C24  0.020
 OS8  plan-2  N4   0.020
 OS8  plan-2  H3   0.020
 OS8  plan-2  H6   0.020
 OS8  plan-2  H7   0.020
 OS8  plan-3  C4   0.020
 OS8  plan-3  C5   0.020
 OS8  plan-3  N1   0.020
 OS8  plan-3  C3   0.020
 OS8  plan-3  O3   0.020
 OS8  plan-3  H12  0.020
 OS8  plan-4  C11  0.020
 OS8  plan-4  C9   0.020
 OS8  plan-4  C10  0.020
 OS8  plan-4  N2   0.020
 OS8  plan-4  O2   0.020
 OS8  plan-4  H13  0.020

